1. Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India

2. SEP-SBI074-CP3-03 Introduction Programmes and Courses SEP –SBI074-CP3- U03

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari Faculty YCMOU Nagpur Centre, Faculty LAD college P.G. D of Biotechnology Research officer Ankur Seeds Pvt Ltd sonalisa_alkari@yahoo.co.in Sonalisaal@rediffmail.com 3© 2008, YCMOU. All Rights Reserved.

4. School of Science and Technology, Online Counseling Resource… © 2008, YCMOU. All Rights Reserved.4 How to Use This Resource  Counselor at each study center should use this presentation to deliver lecture of 40-60 minutes during Face-To-Face counseling.  Discussion about students difficulties or tutorial with assignments should follow the lecture for about 40-60 minutes.  Handouts (with 6 slides on each A4 size page) of this presentation should be provided to each student.  Each student should discuss on the discussion forum all the terms which could not be understood. This will improve his writing skills and enhance knowledge level about topics, which shall be immensely useful for end exam.  Appear several times, for all the Self-Tests, available for this course.  Student can use handouts for last minutes preparation just before end exam.

5. School of Science and Technology, Online Counseling Resource… © 2008, YCMOU. All Rights Reserved.5 Learning Objectives  After studying this module, you should be able to: Describe tertiary structure of protein in details Describe types of bonds Discuss why tertiary structure is important? Describe quaternary structure Describe protein domain

6. School of Science and Technology, Online Counseling Resource… Tertiary Structure-1  In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.  Tertiary structure is considered to be largely determined by the protein's primary structure, or the sequence of amino acids of which it is composed.  Efforts to predict tertiary structure from the primary structure are known generally as protein structure prediction. 6© 2008, YCMOU. All Rights Reserved.

7. School of Science and Technology, Online Counseling Resource… Tertiary Structure-2  However, the environment in which a protein is synthesized and allowed to fold are significant determinants of its final shape and are usually not directly taken into account by current prediction methods.  Most such methods rely on comparisons between the sequence to be predicted and sequences of known structure in the Protein Data Bank and thus account for environment indirectly, assuming the target and template sequences share similar cellular contexts.  A large-scale experiment known as CASP directly compares the performance of state-of-the-art prediction methods and is run once every two and a half years. 7© 2008, YCMOU. All Rights Reserved.

8. School of Science and Technology, Online Counseling Resource… Bond Types Stabilizing Tertiary Structure The kinds of bonds that can exist between the side groups include:  Van der Waals bonds if the side groups are nonpolar.  Hydrogen bonds if the side groups contain hydroxyl or amino groups.  Ionic bonds if the side groups are acids and bases that can transfer protons from one to another making a carboxylate ion, which is negative, and essentially an ammonium or quaternary ammonium ion which is positive.  Covalent bonds if the side groups are cysteine residues in which the sulfur atoms are bonded together by the removal of two hydrogen atoms. 8© 2008, YCMOU. All Rights Reserved.

9. School of Science and Technology, Online Counseling Resource… Tertiary Structure is Important-1  The function of a protein (except as food) depends on its tertiary structure. If this is disrupted, the protein is said to be denatured, and it loses its activity. Examples:  Denatured enzymes lose their catalytic power  Denatured antibodies can no longer bind antigen  A mutation in the gene encoding a protein is a frequent cause of altered tertiary structure.  The mutant versions of proteins may fail to reach their proper destination in the cell and/or be degraded. 9© 2008, YCMOU. All Rights Reserved.

10. School of Science and Technology, Online Counseling Resource… Tertiary Structure is Important-2  Most cases of cystic fibrosis are caused failure of the mutant CFTR protein to reach its destination in the plasma membrane.  Diabetes insipidus is caused by improper folding of mutant versions of V2 - the vasopressin (ADH) receptor oraquaporin © 2008, YCMOU. All Rights Reserved.10

11. School of Science and Technology, Online Counseling Resource… Experimental Determination  The majority of protein structures known to date have been solved with the experimental technique of X-ray crystallography, which typically provides data of high resolution but provides no time-dependent information on the protein's conformational flexibility.  A second common way of solving protein structures uses NMR, which provides somewhat lower-resolution data in general and is limited to relatively small proteins, but can provide time- dependent information about the motion of a protein in solution.  More is known about the tertiary structural features of soluble globular proteins than about membrane proteins because the latter class is extremely difficult to study using these methods. 11© 2008, YCMOU. All Rights Reserved.

12. School of Science and Technology, Online Counseling Resource… Quaternary Structure-1  In biochemistry, quaternary structure is the arrangement of multiple folded protein molecules in a multi-subunit complex.  Many proteins are actually assemblies of more than one polypeptide chain, which in the context of the larger assemblage are known as protein subunits.  In addition to the tertiary structure of the subunits, multiple-subunit proteins possess a quaternary structure, which is the arrangement into which the subunits assemble. 12© 2008, YCMOU. All Rights Reserved.

13. School of Science and Technology, Online Counseling Resource… Quaternary Structure-2  The quaternary protein structure involves the clustering of several individual peptide or protein chains into a final specific shape.  A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains into a particular geometry. There are two major categories of proteins with quaternary structure - fibrous and globular.  Enzymes composed of subunits with diverse functions are sometimes called holoenzymes, in which some parts may be known as regulatory subunits and the functional core is known as the catalytic subunit. 13© 2008, YCMOU. All Rights Reserved.

14. School of Science and Technology, Online Counseling Resource… Quaternary Structure-3 © 2008, YCMOU. All Rights Reserved.14

15. School of Science and Technology, Online Counseling Resource… Examples: Quaternary Structure  Examples of proteins with quaternary structure include hemoglobin, DNA polymerase, and ion channels.  Other assemblies referred to instead as multiprotein complexes also possess quaternary structure.  Examples include nucleosomes and microtubules. 15© 2008, YCMOU. All Rights Reserved.

16. School of Science and Technology, Online Counseling Resource… Quaternary Structure is Important-3  Changes in quaternary structure can occur through conformational changes within individual subunits or through reorientation of the subunits relative to each other.  It is through such changes, which underlie cooperativity and allostery in "multimeric" enzymes, that many proteins undergo regulation and perform their physiological function. 16© 2008, YCMOU. All Rights Reserved.

17. School of Science and Technology, Online Counseling Resource… Determination of Quaternary Structure  Protein quaternary structure can be determined using a variety of experimental techniques that require a sample of protein in a variety of experimental conditions.  The experiments often provide an estimate of the mass of the native protein and, together with knowledge of the masses and/or stoichiometry of the subunits, allow the quaternary structure to be predicted with a given accuracy.  It is not always possible to obtain a precise determination of the subunit composition for a variety of reasons. 17© 2008, YCMOU. All Rights Reserved.

18. School of Science and Technology, Online Counseling Resource… Quaternary Structure-4 18© 2008, YCMOU. All Rights Reserved.

19. School of Science and Technology, Online Counseling Resource…  A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain.  Each domain forms a compact three-dimensional structure and often can be independently stable and folded.  Many proteins consist of several structural domains. One domain may appear in a variety of evolutionarily related proteins.  Domains vary in length from between about 25 amino acids up to 500 amino acids in length. The shortest domains such as zinc fingers are stabilized by metal ions or disulfide bridges. Protein Domains-1 19© 2008, YCMOU. All Rights Reserved.

20. School of Science and Technology, Online Counseling Resource… Protein Domains-2  Domains are defined as stable units of protein structure that could fold autonomously.  In the past domains have been described as units of:  compact structure (Richardson, 1981);  function and evolution (Bork, 1991);  folding (Wetlaufer, 1973).  Each definition is valid and will often overlap, i.e. a compact structural domain that is found amongst diverse proteins is likely to fold independently within its structural environment. 20© 2008, YCMOU. All Rights Reserved.

21. School of Science and Technology, Online Counseling Resource… Protein Domains-3  Nature often brings several domains together to form multidomain and multifunctional proteins with a vast number of possibilities.  In a multidomain protein, each domain may fulfil its own function independently, or in a concerted manner with its neighbors.  Domains can either serve as modules for building up large assemblies such as virus particles or muscle fibres, or can provide specific catalytic or binding sites as found in enzymes or regulatory proteins. 21© 2008, YCMOU. All Rights Reserved.

22. School of Science and Technology, Online Counseling Resource… Protein Classes  Class is determined according to the secondary structure composition and packing within the structure.  Three major classes are recognised; mainly-alpha, mainly-beta and alpha-beta.  This last class (alpha-beta) includes both alternating alpha/beta structures and alpha+beta structures.  A fourth class is also identified which contains protein domains which have low secondary structure content. 22© 2008, YCMOU. All Rights Reserved.

23. School of Science and Technology, Online Counseling Resource… Advantage of Domains in Protein Folding-1  The organization of large proteins by structural domains represents an advantage for protein folding, with each domain being able to individually fold, accelerating the folding process and reducing a potentially large combination of residue interactions.  Furthermore, given the observed random distribution of hydrophobic residues in proteins, domain formation appears to be the optimal solution for a large protein to bury its hydrophobic residues while keeping the hydrophilic residues at the surface. 23© 2008, YCMOU. All Rights Reserved.

24. School of Science and Technology, Online Counseling Resource… Advantage of Domains in Protein Folding-2  However, the role of inter-domain interactions in protein folding and in energetics of stabilisation of the native structure, probably differs for each protein.  In T4 lysozyme, the influence of one domain on the other is so strong that the entire molecule is resistant to proteolytic cleavage.  In this case, folding is a sequential process where the C-terminal domain is required to fold independently in an early step, and the other domain requires the presence of the folded C- terminal domain for folding and stabilisation. 24© 2008, YCMOU. All Rights Reserved.

25. School of Science and Technology, Online Counseling Resource… Domains and Protein Flexibility- 1  The presence of multiple domains in proteins gives rise to a great deal of flexibility and mobility. One of the largest observed domain motions is the `swivelling' mechanism in pyruvate phosphate dikinase.  The phosphoinositide domain swivels between two states in order to bring a phosphate group from the active site of the nucleotide binding domain to that of the phosphoenolpyruvate/pyruvate domain.  The phosphate group is moved over a distance of 45A involving a domain motion of about 100 degrees around a single residue. 25© 2008, YCMOU. All Rights Reserved.

26. School of Science and Technology, Online Counseling Resource… Domains and Protein Flexibility-2 Domain motions are important for: catalysis; regulatory activity; transport of metabolites; formation of protein assemblies and cellular locomotion.  In enzymes, the closure of one domain onto another captures a substrate by an induced fit, allowing the reaction to take place in a controlled way.  Such motions can be observed when two or more crystallographic 3D structures of a protein are experimentally determined in alternate environments, or from the analysis of nuclear magnetic resonance (NMR) derived structures. 26© 2008, YCMOU. All Rights Reserved.

27. School of Science and Technology, Online Counseling Resource… What You Learn…  You have learnt :  The tertiary structure of a protein is its three- dimensional structure, as defined by the atomic coordinates.  The vanderwall forces, hydrogen bond, ionic covalent and covalent forces etc are involved in stabilizing the tertiary structure of protein.  The experimental technique of X-ray crystallography and NMR techiques are involved in elucidation of the 3D structure of proteins.  Quaternary structure is the arrangement of multiple folded protein molecules in a multi- subunit complex.  A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. 27© 2008, YCMOU. All Rights Reserved.

28. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Describe in details tertiary structure of protein? 2.State the importance of tertiary structure.. 3.Describe quaternary structure of protein. 4.What is protein domain? © 2008, YCMOU. All Rights Reserved.28

29. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.The tertiary structure of a protein is its three- dimensional structure, as defined by the atomic coordinates. 2.The function of a protein (except as food) depends on its tertiary structure. 3.The quaternary protein structure involves the clustering of several individual peptide or protein chains into a final specific shape. 4.A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. © 2008, YCMOU. All Rights Reserved.29

30. School of Science and Technology, Online Counseling Resource… Study Tips:1  Book1 Title: Molecular Cell Biology Author: Harvey Lodish, David Baltimore Publisher:Publishers: W. H. Freeman and Company  Book2 Title: Principles of Biochemistry Author: AlbertL Lehninger Publisher:CBS Publishers & Distributors 30© 2008, YCMOU. All Rights Reserved.

31. School of Science and Technology, Online Counseling Resource… Study Tips:2  Book3 Title: Biochemistry Author: Lubert stryer Publishers: Freeman International  Book4 Title: Biochemistry Author: Keshav Trehan Publishers: Wiley Eastern 31© 2008, YCMOU. All Rights Reserved.

32. School of Science and Technology, Online Counseling Resource… Study Tips www.en.wikipedia.org Microsoft Encarta Encyclopedia http://en.wikipedia.org/wiki/ Wikipedia the free encyclopedia 32© 2008, YCMOU. All Rights Reserved.

33. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You 33© 2008, YCMOU. All Rights Reserved.